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 Application Catalog |
Amber PMEMD-parallel
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PMEMD (Particle Mesh Ewald Molecular Dynamics) is a reimplementation of a subset of sander functionality that has been written with the major goal of improving the performance of the most frequently used methods of sander.
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Category: Life Sciences
Sub Category: Computational Chemistry
Publisher: University of California, San Francisco
Date Published: March 2006
Version: 9
Pricing: Amber 9 License Agreement
Runtime: $1/CPU-hr.
What is a CPU-hr.?
A CPU-hr. is the aggregate CPU time spent across all machines, rounded up to the nearest hour (e.g., a task running on 1,000 CPUs for one minute = 1,000 CPU minutes or approximately 17 CPU hours, costing you only $17).
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Key Features
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- PMEMD supports Particle Mesh Ewald simulations, Generalized Born simulations, and ALPB (Analytical Linearized Poisson-Boltzmann) simulations.
- The performance and scaling for PME simulations are typically significantly better than that attained by sander.
- In comparison to sander, PMEMD runs more rapidly, scales better on parallel processors using MPI, can be used profitably on significantly higher numbers of processors, and uses less resident memory.
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Description |
PMEMD is ideal for molecular dynamics simulations of large solvated systems for long periods of time, especially if supercomputer resources are available. PMEMD is an extensively modified version of the sander program, optimized for periodic, PME simulations, and for GB simulations. It is faster, and scales better on parallel machines, than sander; hence it is generally the program of choice, unless you need options that it does not support. Sander is the vehicle to explore new features, and PMEMD is a "production" code that implements sander's most-used features in a well-tested fashion that performs well in high-performance environments.
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Technical Information |
PMEMD accepts Amber 9 sander input files (mdin, prmtop, inpcrd, refc), and is also backward compatible in regard to input to the same extent as sander 9. You will need Fortran 95, C and C++ compilers. |
Publisher Information |
University of California, San Francisco
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Pricing and Payment Information |
License: Amber 9 License Agreement
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